Results Of Molecular Dynamics Simulations Research Articles

Microscopic mechanism study and process optimization of dimethyl carbonate production coupled biomass chemical looping gasification system

Biomass chemical looping gasification technology is one of the essential ways to utilize abundant biomass resources. At the same time, dimethyl carbonate can replace phosgene as an environment-friendly organic material for the synthesis of polycarbonate. In this paper, a novel system coupling biomass chemical looping gasification with dimethyl carbonate synthesis with methanol as an intermediate is designed through microscopic mechanism analysis and process optimization. Firstly, reactive force field molecular dynamics simulation is performed to explore the reaction mechanism of biomass chemical looping gasification to determine the optimal gasification temperature range. Secondly, steady-state simulations of the process based on molecular dynamics simulation results are carried out to investigate the effects of temperature, steam to biomass ratio, and oxygen carrier to biomass ratio on the syngas yield and compositions. In addition, the main energy indicators of biomass chemical looping gasification process including lower heating value and cold gas efficiency are analyzed based on the above optimum parameters. Then, two synthesis stages are simulated and optimized with the following results obtained: the optimal temperature and pressure of methanol synthesis stage are 150 °C and 4 MPa; the optimal temperature and pressure of dimethyl carbonate synthesis stage are 140 °C and 0.3 MPa. Finally, the pre-separation-extraction-decantation process separates the mixture of dimethyl carbonate and methanol generated in the synthesis stage with 99.11% purity of dimethyl carbonate. Above results verify the feasibility of producing dimethyl carbonate from the perspective of multi-scale simulation and realize the multi-level utilization of biomass resources.

SCREENING OF ASHITABA (ANGELICA KEISKEI K.) COMPOUNDS AS POTENTIAL MYCOBACTERIUM TUBERCULOSIS KASA INHIBITORS

Objective: Tuberculosis (TB) is a major global issue, mainly owing to the emergence of antibiotic-resistant strains of the disease's causative agent, Mycobacterium tuberculosis. The current standard of treatment for tuberculosis entails a prolonged course of antibiotics with toxic side effects and is accompanied by low patient compliance. Therefore, developing and discovering TB medications is critical to obtaining TB drugs that are more effective and sensitive to Mycobacterium tuberculosis. Ashitaba (Angelica keiskei K.) has reported that Ashitaba extract and chalcone have anti-TB properties, but the responsible compound has not been reported yet. This study aimed to identify the profile metabolites present in Ashitaba and their interaction with Mycobacterium tuberculosis KasA.
 Methods: To suggest these, we used molecular docking and molecular dynamic to predict the interactions of 40 selected compounds from the Ashitaba against Mycobacterium tuberculosis KasA (PDB ID 2WGE).
 Results: The results of molecular docking identified the top two compounds as xanthoangelol I (XAI) and (2E)-1-[4-hydroxy-2-(2-hydroxy-2-propanyl)-2,3-dihydro-1-benzofuran-7-yl]-3-(4-hydroxyphenyl)-2-propen-1-one (4HH), with bond free energies of-12.03 and-11.87 kcal/mol, respectively. Based on the results of molecular dynamics simulations, the XAI was stronger than 4HH in stabilizing complexes with 2WGE with total energy (ΔGbind, MMGBSA) of-54.8512 and-37.8836 kcal/mol, respectively.
 Conclusion: It can be concluded that xanthoangelol I (XAI) have the most potent inhibitor of Mycobacterium tuberculosis KasA.

IDENTIFICATION OF FLAVONOIDS FROM ACALYPHA INDICA L. (EUPHORBIACEAE) AS CASPASE-3 ACTIVATORS USING MOLECULAR DOCKING AND MOLECULAR DYNAMICS

Objective: The purpose of this study was to determine the structural-based molecular interactions between flavonoids contained in Acalypha indica L. and caspase-3 by molecular docking and molecular dynamics (MD) simulations.
 Methods: In a computer simulation, ten flavonoids contained in A. indica L. were evaluated for caspase-3 using the X-ray crystal structure of human caspase-3 (PDB ID 1NME). The AutoDock 4.2 software was used to study molecular docking, and MD simulations were done with GROMACS v2018.
 Results: The results of molecular docking identified the top four compounds, namely nicotiflorin, naringenin, hesperetin, and kaempferol, with docking scores of-6.81,-6.45,-6.33, and-6.10 kcal/mol, respectively. According to the MD simulation results, nicotiflorin was most effective in stabilizing the complex with caspase-3, with a total energy (ΔGbind, MM-PBSA) of-96.315 kcal/mol.
 Conclusion: This study showed that nicotiflorin was the flavonoid in A. indica L. that activated caspase-3 the best.

Design, Synthesis, Inhibitory Activity, and Molecular Modeling of Novel Pyrazole-Furan/Thiophene Carboxamide Hybrids as Potential Fungicides Targeting Succinate Dehydrogenase

To discover new fungicides targeting succinate dehydrogenase (SDH), 36 new furan/thiophene carboxamides containing 4,5-dihydropyrazole rings were designed, synthesized, and characterized. The crystal structure of compound 5l was determined with the X-ray diffraction (XRD) of single crystals. The antifungal activity of these compounds was studied against Botrytis cinerea, Pyricularia oryzae, Erysiphe graminis, Physalospora piricola, and Penicillium digitatum. Bioassay results were that most compounds had obvious inhibitory activity at 20 μg/mL. Compounds 5j, 5k, and 5l possessed outstanding inhibitory activity against B. cinerea. Their EC50 values were 0.540, 0.676, and 0.392 μg/mL, respectively. They owned better effects than fluxapyroxad (EC50 = 0.791 μg/mL). In the meantime, the inhibitory activity of 16 compounds was evaluated against SDH. It turned out that these compounds displayed excellent activity. The IC50 values of compounds 5j, 5k, and 5l reached 0.738, 0.873, and 0.506 μg/mL, respectively, whereas the IC50 value of fluxapyroxad was 1.031 μg/mL. The results of molecular dynamics (MD) simulation showed that compound 5l possessed a stronger affinity to SDH than fluxapyroxad.

A 5'-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA.

Methyl CpG binding proteins (MBPs) are transcription factors that recognize the methylated CpG sites in DNA and mediate the DNA methylation signal into various downstream cellular processes. The C2H2 zinc finger (ZF) protein, Kaiso, also an MBP, preferentially binds to two symmetrically methylated CpG sites in DNA sequences via C-terminal C2H2 ZF domains and mediates the transcription regulation process. Investigation of the molecular mechanism of the recognition of methylated DNA (meDNA) by Kaiso is important to understand how this protein reads and translates this methylation signal into downstream transcription outcomes. Despite previous studies in Kaiso-meDNA interactions, detailed structural investigations on the sequence-specific interaction of Kaiso with the meDNA sequence are still lacking. In this work, we used molecular modeling and molecular dynamics (MD) simulation-based computational approaches to investigate the recognition of various methylated DNA sequences by Kaiso. Our MD simulation results show that the Kaiso-meDNA interaction is sequence specific. The recognition of meDNA by Kaiso is enhanced in the MeECad sequence compared to the MeCG2 sequence. Compared to the 5'-flanking T/A pair in MeCG2, both MeCG2_mutCG and MeECad sequences show that a C/G base pair allows GLU535 of Kaiso to preferably recognize and bind the core mCpG site. The core mCGmCG site is crucial for the recognition process and formation of a stable complex. Our results reveal that the 5'-flanking nucleotides are also important for the enhanced binding and recognition of methylated sites.

Interaction of Components of Epoxy Composite Containing Carbon Nanotubes and Graphene Oxide Mixture

Mixtures of carbon nanotubes (CNTs) and graphene oxide (GO) in composite materials often exhibit synergistic effects with respect to mechanical and electrophysical properties. In this paper, the mechanisms of interaction between CNTs, GO and epoxydian resin macromolecules were discussed based on the results of molecular dynamics simulations. Calculations were performed in the MM3 force field at exposure times up to 100 ps. The influence of the CNT’s graphene layers shape and the presence of oxygen-containing functional groups on the self-assembly process during the epoxy composite formation has been demonstrated. It is shown that graphene oxide sheets are arranged around cylindrical nanotubes and envelop them, while when using tapered nanotubes, the formation of alternating layers of CNTs and GO should be expected. The presence of oxygen-containing groups on the surface of cylindrical nanotubes promotes the penetration of epoxydian resin macromolecules into the space between CNTs and GO. The simulation results of the "cylindrical CNTs - GO" and the "conical CNTs - GO" hybrid particles were confirmed by scanning electron microscopy data.

Feasibility and mechanism analysis of Reduning in the prevention of sepsis-induced pulmonary fibrosis.

Introduction: The increasing mortality in patients with sepsis-induced pulmonary fibrosis owes to a lack of effective treatment options. This study aims to explore the possibility and possible targets of Reduning in the prevention of sepsis-related pulmonary fibrosis. Methods: The active components and targets of Reduning were searched and screened from the database and analysis platform of traditional Chinese medicine (TCM) system pharmacology. GeneCards, human genome database, DisGeNET database, and the OMIM database were checked to determine the targets associated with sepsis-induced pulmonary fibrosis. DAVID Bioinformatics Resources 6.8 was used for GO and KEGG enrichment analysis to predict its possible signaling pathways and explore its molecular mechanism. The protein-protein interaction (PPI) network was used to identify key active components and core targets. Molecular docking technology was applied to screen the complexes with stable binding of key active components and core targets. Molecular dynamics simulations were used to verify the binding stability and molecular dynamics characteristics of the complexes. The protective effect of RDN on sepsis-induced pulmonary fibrosis was verified by in vitro and in vivo experiments. Results: There were 319 shared targets between sepsis-induced pulmonary fibrosis and RDN. GO enrichment analysis showed that they mainly regulated and participated in the positive regulation of kinase activity, mitogen-activated protein kinase (MAPK) cascade, and protein phosphorylation. KEGG enrichment analysis showed that they were mainly enriched in the mitogen-activated protein kinase cascade signaling pathway, the calcium signaling pathway, the apoptosis pathway, and other signaling pathways. The results of molecular docking and molecular dynamics simulations showed that the active components, stigmasterol, beta-sitosterol, and quercetin, had good binding activities with ERBB2, and they exhibited good stability. Molecular validation experiments confirmed RDN could alleviate lung fibrosis induced by cecum ligation and puncture (CLP), in parallel with the inhibition of the ERBB2-p38 MAPK pathway in mouse alveolar macrophages (AMs). Discussion: Reduning may prevent sepsis-induced pulmonary fibrosis by regulating the ERBB2-p38 MAPK signaling pathway, which provides a possibility for the prevention of sepsis-induced pulmonary fibrosis with traditional Chinese medicine.

Density Functional Theory Study on Antioxidant Activity of Three Polyphenols.

In recent years, research on the antioxidant activity of natural antioxidants has become more and more popular. Polyphenols are a large number of natural antioxidants in plants. This paper selected three common polyphenols to study their antioxidant activity based on quantum chemistry theory. This experiment hopes to provide a theoretical basis for the further development of polyphenol health food with strong antioxidant activity. Three polyphenols resveratrol, liquiritigenin, and isoliquiritigenin were optimized at the level of B3lyp/6-311G (d, p), and the single point energy was calculated with B3lyp/6-311 + + G (2d, 2p). The phenol hydroxyl bond dissociation enthalpy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE) were calculated in different phase states study the antioxidant mechanism. Draw the frontier molecular orbital and conduct dynamic simulation analysis scavenging · OH and · OOH to explore the most possible active sites in different phenolic hydroxyl sites. The bond length, dihedral angle, BDE, IP, PDE, PA and ETE were compared to speculate the antioxidant activity: Resveratrol > isoliquiritigenin > liquiritigenin. By analyzing the frontier molecular orbital and dynamic simulation results, it is speculated that the phenolic hydroxyl groups at C4', C4', and C4 are the most likely active sites of resveratrol, liquiritigenin, and isoliquiritigenin, respectively. In different phase states, the three compounds showed the same antioxidant activity, and the phenolic hydroxyl activities of the three compounds were different at different sites.

Virtual screening and molecular dynamics simulation studies to predict the binding of Sisymbrium irio L. derived phytochemicals against Staphylococcus aureus dihydrofolate reductase (DHFR)

The discovery of antibiotics initiated the era of drug innovation and implementation for human and animal health. Very soon, antibiotic resistance started evolving due to over-prescription and heavy usage of drugs leading to deleterious side effects. However, using plant extracts or medicinal plants has emerged as a new approach to dealing with the current problem. One such medicinal plant Sisymbrium irio L. is widely used in Unani therapy as an antimicrobial, analgesic, antipyretic, antioxidant, anti-inflammatory, hepatoprotective, bronchoprotective etc. The phytochemicals extracted from the aerial part of the plant have been used as a natural compound library and screened against a well-known anti-bacterial drug target Dihydrofolate reductase (DHFR) enzyme of Staphylococcus aureus. The top two phytochemicals with lower docking score along with the positive control were subjected to molecular dynamics (MD) simulation studies to examine the stabilities of the complexes over 100 ns, followed by binding free energy estimation. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and Radius of Gyration (Rg) yielded established results throughout the MD run. Moreover, the derived phytochemicals exhibited lower binding free energy values than the positive control that can be tested for its in vitro efficacy, followed by further optimization to attain a potent therapeutic against S. aureus. Taken together, the present study suggests two promising phytochemicals derived from the aerial part of the plant S. irio with stable MD simulation results, strong binding affinity and no side effects.

Gating and modulation of an inward-rectifier potassium channel.

Inward-rectifier potassium channels (Kirs) are lipid-gated ion channels that differ from other K+ channels in that they allow K+ ions to flow more easily into, rather than out of, the cell. Inward rectification is known to result from endogenous magnesium ions or polyamines (e.g., spermine) binding to Kirs, resulting in a block of outward potassium currents, but questions remain regarding the structural and dynamic basis of the rectification process and lipid-dependent channel activation. Here, we present the results of long-timescale molecular dynamics simulations starting from a crystal structure of phosphatidylinositol 4,5-bisphosphate (PIP2)-bound chicken Kir2.2 with a non-conducting pore. After introducing a mutation (G178R) that is known to increase the open probability of a homologous channel, we were able to observe transitions to a stably open, ion-conducting pore, during which key conformational changes occurred in the main activation gate and the cytoplasmic domain. PIP2 binding appeared to increase stability of the pore in its open and conducting state, as PIP2 removal resulted in pore closure, with a median closure time about half of that with PIP2 present. To investigate structural details of inward rectification, we simulated spermine binding to and unbinding from the open pore conformation at positive and negative voltages, respectively, and identified a spermine-binding site located near a previously hypothesized site between the pore cavity and the selectivity filter. We also studied the effects of long-range electrostatics on conduction and spermine binding by mutating charged residues in the cytoplasmic domain and found that a finely tuned charge density, arising from basic and acidic residues within the cytoplasmic domain, modulated conduction and rectification.

Interaction between PEO and Kaolinite in Flocculating: An Experimental and Molecular-Simulation Study

In this paper, the flocculation properties of polyethylene oxide (PEO) on kaolinite and the mechanism of adsorption on kaolinite anisotropic substrates were explored. As revealed by the experimental results, the settling rate and removal rate of kaolinite increased with increasing PEO concentration, but too high PEO concentration would cause the small particles to stabilize and become difficult to settle. Furthermore, to probe deep into the interactions between PEO and kaolinite anisotropic substrates, the morphology of adsorbed PEO, interfacial adsorption structure, and dynamic behavior of water molecules were determined by quartz crystal microbalance with dissipation (QCM-D) and molecular dynamics (MD) simulations. The adsorption amount of PEO on different mineral surfaces is in the order of kaolinite > alumina > silica, and the thickness of the adsorption structure formed by alumina is greater than that of silica. As illustrated by the MD simulation results, the adsorption of PEO reduces the concentration of water molecules attached to the kaolinite surface. The PEO forms a double-layer adsorption structure on the 001 surface, while forming a tight monolayer adsorption structure on the 001¯ surface, weakening the interaction between the surface and the water molecules. The above results demonstrate that the adsorption of PEO effectively weakened the hydration dispersion of kaolinite and promoted the agglomeration of kaolinite particles.

Investigation of the interaction between glucose-6-phosphate dehydrogenase and ATA-inhibitor by molecular docking and molecular dynamics simulation

Human glucose-6-phosphate dehydrogenase (G6PD) is a kind of polymerase, which can bind cofactors β-D-glucose-6-phosphate (G6P) and catalyzes NADP+ to produce NADPH. Therefore, G6PD plays a crucial role in maintaining reduced glutathione to protect cells from oxidative stress disorders. Aurine tricarboxylic acid (ATA) is a potential metal binding inhibitor. Here, we found that G6P and ATA have a common potential binding site in the G6PD receptor conformation through molecular docking. The results of molecular dynamics (MD) simulation showed that, compared with apo-G6PD, G6P-G6PD and ATA-G6PD had lower root mean square deviation (RMSD), radius of gyration (Rg), and solvent accessible surface area (SASA), indicating that binding ligand molecules could promote the overall conformation of G6PD to be more stable. These results suggest that ATA may compete for the binding sites of G6P, thereby inhibiting the catalytic function of G6PD. This study revealed the mechanism of interaction between ATA inhibitors and G6PD at the atomic conformation level, providing a theoretical basis for investigating the effects of cellular oxidative stress.

RSM models approach for optimization of the mechanical properties of electroless Ni-B-nanodiamond coating: An experimental and molecular dynamic simulation study

This report explores the effects of electroless Ni-B-nanodiamond plating bath parameters for optimization of the hardness and deposition rate based on response surface method (RSM). Quadratic models were developed and found to be mathematically appropriate for the optimization. The nanodiamonds (ND) and optimized coating were characterized using XPS, DLS, FIB-SEM, GDOES, microhardness, and nanoindentation. The results of the molecular dynamic simulation show low adsorption energy of borohydride on nanodiamonds surface is not favourable for borohydride dehydrogenation, therefore the boron content of the coating decreases when ND are added. Raman spectroscopy, SEM, and EDS analysis carried out on different zones of the surface after scratch test show nanodiamonds undergo graphitization and micro-cracking which block crack propagation at lower load. In addition, ND improves formation of the tribolayer at higher loads. The Raman spectroscopy results after indentation tests show the possibility of SP3 to SP2 phase transformation for nanodiamonds. The molecular dynamic simulation results confirm that phase transformation through monitoring the changes in nanodiamonds interatomic potential and interatomic distances. It is believed that the volume expansion caused by this phase transformation increases the toughness of coating.

Insights into magma ocean dynamics from the transport properties of basaltic melt.

The viscosity of magma plays a crucial role in the dynamics of the Earth: from the crystallization of a magma ocean during its initial stages to modern-day volcanic processes. However, the pressure-dependence behavior of viscosity at high pressure remains controversial. In this study, we report the results of first-principles molecular dynamics simulations of basaltic melt to show that the melt viscosity increases upon compression along each isotherm for the entire lower mantle after showing minima at ~6 GPa. However, elevated temperatures of the magma ocean translate to a narrow range of viscosity, i.e., 0.01-0.03 Pa.s. This low viscosity implies that the crystallization of the magma ocean could be complete within a few million years. These results also suggest that the crystallization of the magma ocean is likely to be fractional, thus supporting the hypothesis that present-day mantle heterogeneities could have been generated during the early crystallization of the primitive mantle.

Spreading Behavior and Wetting Characteristics of Anionic Surfactant Droplets Impacting Bituminous Coal.

Spraying water-based materials on the coal surface is a common means of coal dust suppression. There are obvious dynamic wetting behaviors during droplets impacting coal. To explore the spreading behavior and wetting characteristics of anionic surfactant droplets on bituminous coal, three anionic surfactants, which are sodium dodecyl sulfate (SDS), sodium dodecyl sulfonate (SDDS), and sodium dodecyl benzene sulfonate (SDBS), were used for the droplet impact experiment and molecular dynamics (MD) simulation. The results show that the addition of anionic surfactants can promote the wetting behavior of the droplet, and the difference between the head group and the tail group of the surfactant molecules can affect the wettability of the droplet. The dimensionless spreading coefficient shows the rule of SDBS > SDS > SDDS. When the concentration does not reach critical micelle concentration (CMC), the surface tension decreases and the dimensionless spreading coefficient of droplets increases with the increase of concentration. When the droplet concentration reaches the CMC, surface tension is no longer an effective indicator to evaluate the wettability of droplets. The dimensionless spreading coefficient can effectively evaluate the macroscopic spreading wetting behavior of droplets, and it is better than the surface tension. MD simulation results show that the interaction between anionic surfactants and coal molecules can affect the adsorption behavior, and the interaction energy and adhesion work are shown as the rule of SDBS < SDS < SDDS. The results of MD simulation and the impact experiment show that the intermolecular adsorption behavior has a significant influence on the spreading process. The results of MD simulation further explain the results of the droplet impact experiment.

Molecular dynamics simulations and X-ray scattering show the κ-carrageenan disorder-to-order transition to be the formation of double-helices

Recent molecular dynamics simulations, verified experimentally by solution-state x-ray scattering experiments, have found that κ-carrageenan chains contain helical secondary structure, akin to that found in the solid-state, even in aqueous solution. Furthermore, upon the addition of ions to single chains the simulations found no evidence that any conformational transitions take place. These findings challenge the long-held assumption that the so-called disorder-to-order transition in carrageenan systems involves a uni-molecular ‘coil-to-helix transition’. Herein, the results of further molecular dynamics simulations undertaken using pairs of κ-carrageenan chains in 0.1 M NaI solutions are reported, and are validated experimentally using state-of-the-art solution-state WAXS experiments. From initially separated chains double-helices are shown to form, leading the authors to propose ‘two single helices-to-stabilized double-helix’ as a description of the molecular events taking place during the disorder-to-order transition.

Anti-inflammatory biomolecular activity of chlorinated-phenyldiazenyl-naphthalene-2-sulfonic acid derivatives: perception from DFT, molecular docking, and molecular dynamic simulation

In this study, two novel derivatives of naphthalene-2-sulfonic acid: 6-(((1S,5R)-3,5-dichloro-2,4,6-triazabicyclo [z3.1.0]hex-3-en-1-yl)amino)-5-((E)-phenyldiazenyl)naphthalene-2-sulfonic acid (DTPS1) and (E)-6-((4,6-dichloro-1,3,5-triazine2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2-sulfonic acid (DTPS2) have been synthesized and characterized using FT-IR, UV-vis, and NMR spectroscopic techniques. Applying density functional theory (DFT) at the B3LYP, APFD, PBEPBE, HCTH, TPSSTPSS, and ωB97XD/aug-cc-pVDZ level of theories for the electronic structural properties. In-vitro analysis, molecular docking, molecular dynamic (MD) simulation of the compounds was conducted to investigate the anti-inflammatory potential using COXs enzymes. Docking indicates binding affinity of −9.57, −9.60, −6.77 and −7.37 kcal/mol for DTPS1, DTPS2, Ibuprofen and Diclofenac which agrees with in-vitro assay. Results of MD simulation, indicates sulphonic group in DTPS1 has > 30% interaction with the hydroxyl and oxygen atoms in amino acid residues, but > 35% interaction with the DTPS2. It can be said that the DTPS1 and DTPS2 can induce inhibitory effect on COXs to halt biosynthesis of prostaglandins (PGs), a chief mediator of inflammation and pain in mammals. Communicated by Ramaswamy H. Sarma

A novel approach to bio-mineralization of electrospun PCL scaffolds by protein and hydroxyapatite nanoparticles; molecular dynamics simulation and in-vitro evaluation

The nano-fibrous polycaprolactone (PCL) scaffolds are one of the promising materials for bone tissue engineering. However, the role of protein in the bio-mineralization of PCL fibers is not clear. This study aims to find how a protein (e.g. bovine serum albumin (BSA)) is attached to the hydroxyapatite (HA) nanoparticles (NPs) loaded on the PCL fiber, and it affected the bio-mineralization of a hybrid scaffold. The molecular dynamic (MD) simulation was utilized to explore the protein and HA attachment. The results of MD simulation indicated that the a(b)-planes of HA crystal and glutamic acid (Glu) from BSA molecule have critical roles in attachment together. In the following, the electrospinning method was applied to synthesize the pristine and hybrid PCL scaffolds to evaluate the MD results. The scanning electron microscopy (SEM) images showed that BSA could be successfully attached to the HA NPs, and coiled around the PCL-HA junction confirming the MD simulation. To evaluate the bio-mineralization, the in-vitro immersion test in the simulation body fluid (SBF) solution and the cytocompatibility of scaffolds by the MG63 osteosarcoma cells were studied. The results indicated better osteoconduction and bone regeneration for the hybrid PCL- BSA-HA scaffold because of the synergic effects of HA NPs and BSA protein.

Elaboration of entropy with glass composition: A molecular dynamics study

Recently, entropy was proposed as a simple input into glass science and engineering, which has an interesting relationship with the glass properties containing glass transition temperature (T g ), melting point, and concentration of non-bridging oxygens (NBOs). In the current study, molecular dynamics (MD) simulation as the powerful method was used to approve the recently observed relations. In this regard, various silicate-based compositions containing 25, 30, and 35 mol% of alkaline earth oxides were simulated. The T g , bond length, and the concentration of NBOs were evaluated using MD simulation results, including volume-temperature curves and radial distribution functions (RDF) results. According to the results, T g values of the simulated glass were reduced up to 400 K by increasing the amounts of additives up to 35 mol%. The distance between Si and O species as the glass former basis increased from 1.580, 1.591, 1.608, and 1.615 Å to 1.590, 1.596, 1.616, and 1.621 Å, in the SsiO 2 -MgO, SiO 2 -SrO, SiO 2 -CaO, SiO 2 -SrO, and SiO 2 -BaO systems, respectively. Besides, as found from the results, increasing the concentration of additives increases the mobility of Si-O paired atoms. Accordingly, the glass disorderliness or entropy of the systems increases with adding glass modifiers. Also, the concentration of NBOs in the mentioned systems was 35.9-56.3, 36.8-57.5, 26.1-43.9, and 18.2-29.7%. The results of NBOs confirm that the glass disordering increases by increasing amounts of additives. In summary, using MD simulation of silicate glass containing alkaline earth oxides, the relation between entropy as a theoretically calculated property and glass characteristics such as T g is successfully approved.

Molecular Dynamics Simulation of the Thermal Diffusion Effect in n-Alkane Binary Mixtures.

In oil and gas reservoirs, the thermal diffusion effect leads to compositional variations of hydrocarbon fluids in both horizontal and vertical directions. Compared with experimental methods, molecular dynamics (MD) simulations can cover a broader range of pressures and temperatures for the investigation of the thermal diffusion effect. However, previous MD simulations of the thermal diffusion effect for n-alkane binary mixtures have been limited to only nC5-nC10, nC6-nC10, and nC6-nC12 mixtures. In this work, for the first time, we perform a series of MD simulations on n-alkane binary mixtures, C1-C3, C1-nC4, nC7-nC12, nC7-nC16, and nC10-nCi (i = 5, 7, 8, 12, 14, 16), with different mole fractions and temperature and pressure conditions. The boundary-driven nonequilibrium molecular dynamics (BD-NEMD) with the enhanced heat exchange (eHEX) algorithm is used to generate the temperature gradient and measure the thermal diffusion effect. Additionally, a workflow for molecular simulations of thermal diffusion of n-alkane binary mixtures is proposed to ensure their repeatability and reliability. The errors for our MD simulation results are generally less than 10% compared with experimental data. Our results show that in the binary mixture, the heavy component tends to move to the cold region, while the lighter component tends to aggregate near the hot region, which is consistent with experimental observations.